1
|
Azhar Z, Grose RP, Raza A, Raza Z. In silico targeting of colony-stimulating factor-1 receptor: delineating immunotherapy in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:727-742. [PMID: 37711590 PMCID: PMC10497393 DOI: 10.37349/etat.2023.00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/23/2023] [Indexed: 09/16/2023] Open
Abstract
Aim Delineate structure-based inhibition of colony-stimulating factor-1 receptor (CSF1R) by small molecule CSF1R inhibitors in clinical development for target identification and potential lead optimization in cancer therapeutics since CSF1R is a novel predictive biomarker for immunotherapy in cancer. Methods Compounds were in silico modelled by induced fit docking protocol in a molecular operating environment (MOE, MOE.v.2015). The 3-dimensional (3D) X-ray crystallized structure of CSF1R kinase (Protein Databank, ID 4R7H) was obtained from Research Collaboratory for Structural Bioinformatics (RSCB) Protein Databank. The 3D conformers of edicotinib, DCC-3014, ARRY-382, BLZ-945, chiauranib, dovitinib, and sorafenib were obtained from PubChem Database. These structures were modelled in Amber10:EHT molecular force field, and quick prep application was used to correct and optimize the structures for missing residues, H-counts, termini capping, and alternates. The binding site was defined within the vicinity of the co-crystallized ligand of CSF1R kinase. The compounds were docked by the triangular matcher placement method and ranked by the London dG scoring function. The docked poses were further refined by the induced fit method. The pose with the lowest binding score (ΔG) was used to model the ligand interaction profile in Discovery Studio Visualizer v17.2. The co-crystallized ligand was docked in its apo conformation, and root-mean-square deviation was computed to validate the docking protocol. Results All 7 CSF1R inhibitors interact with residue Met637 exhibiting selectivity except for edicotinib. The inhibitors maintain CSF1R in an auto-inhibitory conformation by interacting with Asp797 of the Asp-Phe-Gly (DFG) motif and/or hindering the conserved salt bridge formed between Glu633 and Lys616 thus stabilizing the activation loop, or interacting with tryptophan residue (Trp550) in the juxtamembrane domain. DCC-3014, ARRY-382, BLZ-945, and sorafenib bind with the lowest binding energy with CSF1R kinase. Conclusions Pyrimidines are potent inhibitors that interact with CSF1R residues. DCC-3014 and ARRY-382 exhibit exceptional pharmaceutical potential exhibiting great structural stability and affinity.
Collapse
Affiliation(s)
- Zahra Azhar
- Centre of Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Richard P. Grose
- Centre of Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Afsheen Raza
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, Abu Dhabi 59911, United Arab Emirates
| | - Zohaib Raza
- Department of Chemistry, The University of Adelaide, 5005 Adelaide, South Australia, Australia
| |
Collapse
|
2
|
Pulmonary administration of a CSF-1R inhibitor alters the balance of tumor-associated macrophages and supports first-line chemotherapy in a lung cancer model. Int J Pharm 2021; 598:120350. [PMID: 33545279 DOI: 10.1016/j.ijpharm.2021.120350] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/28/2021] [Accepted: 01/31/2021] [Indexed: 12/14/2022]
Abstract
Lung cancers remain the leading cause of cancer-related death in both men and women. Infiltrating immune cells in the tumor microenvironment (TME) play a critical role in the formation, progression, and the response of solid tumors to therapy, including in lung cancers. Clinical studies have established that tumor-associated macrophages (TAMs) and their phenotypical composition are critical immune infiltrates in the lung TME, with the abundance of the M2-like phenotype negatively correlating with patient survival. Colony-Stimulating Factor 1 (CSF-1) receptor (CSF-1R) is a type III protein tyrosine kinase receptor that plays an important role in the recruitment and differentiation of monocytes into tumor-promoting M2-like TAMs and their survival. In this work we evaluated the therapeutic potential of PLX 3397 (PLX), a small molecule CSF-1R inhibitor (CSF-1Ri), upon local lung administration in an immune-competent mouse model of lung cancer. The efficacy of local lung delivered PLX as single therapy was investigated first. As assessed by immunofluorescence of sections of lung tumor nodules, a statistically significant reduction in M2-like TAMs and an increase in M1-like TAMs was observed, thus leading to a shift in the (M1/M2) balance. Those changes in abundance of immune infiltrates correlated with a significant decrease in tumor burden when compared to control. When combined with systemically administered cisplatin (CIS) PLX treatment provided further benefits, leading to a significant decrease in tumor burden when compared to either PLX or CIS treatments alone, as measured by bioluminescence intensity (BLI) in vivo (thoracic area) and ex vivo (lung tissue). This combination therapy led to the most pronounced increase in M1/M2 ratio, followed by a significant decrease in M2-like TAMs with the CIS therapy. This work is clinically relevant as it demonstrates the potential of local lung administration of PLX to support standard of care chemotherapy for lung cancer management. This is important as the pulmonary route of administration is a plausible strategy for reducing the total dose of CSF-1Ris as the tissue of interest (lungs) can be locally targeted. Because the major off-target effect of CSF-1Ris is liver toxicity, reducing systemic concentration will support translation of those therapies, especially in combination with standard of care chemotherapy that has significant off-target toxicity and patient attrition itself. This work is scientifically relevant as we demonstrate for the first time that local administration of a CSF-1Ri to the lungs leads to a shift in the balance of TAMs in the TME of a model of lung tumor, adding to the sparse literature of CSF-1Ris related to lung cancers.
Collapse
|
3
|
Xun Q, Wang Z, Hu X, Ding K, Lu X. Small-Molecule CSF1R Inhibitors as Anticancer Agents. Curr Med Chem 2020; 27:3944-3966. [PMID: 31215373 DOI: 10.2174/1573394715666190618121649] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 12/20/2022]
Abstract
Persuasive evidence has been presented linking the infiltration of Tumor-Associated Macrophages (TAMs) with the driving force of tumorigenesis and in the suppression of antitumor immunity. In this context CSF1R, the cellular receptor for Colony Stimulating Factor-1 (CSF1) and Interleukin 34 (IL-34), occupies a central role in manipulating the behavior of TAMs and the dysregulation of CSF1R signaling has been implicated in cancer progression and immunosuppression in many specific cancers. Consequently, CSF1R kinase has been a target of great interest in cancer treatment and significant research efforts have focused on the development of smallmolecule CSF1R inhibitors. In this review, we highlight current progress on the development of these small molecule CSF1R inhibitors as anticancer agents. Special attention is paid to the compounds available in advanced clinical trials.
Collapse
Affiliation(s)
- Qiuju Xun
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhen Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xianglong Hu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| |
Collapse
|
4
|
Yoo SS, Kang HG, Choi JE, Hong MJ, Do SK, Lee JH, Lee WK, Lee SY, Lee J, Cha SI, Kim CH, Lee EB, Park JY. The effect of susceptibility variants, identified in never-smoking female lung cancer cases, on male smokers. Korean J Intern Med 2020; 35:929-935. [PMID: 31878769 PMCID: PMC7373985 DOI: 10.3904/kjim.2018.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/13/2019] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND/AIMS Genome wide and candidate gene association studies have identified polymorphisms associated with the risk of lung cancer in never-smokers. This study was conducted to evaluate the association between 11 polymorphisms identified in female never smokers and the lung cancer risk in male smokers. METHODS This study included 714 lung cancer patients and 626 healthy controls. The polymorphisms were genotyped using SEQUENOM MassARRAY iPLEX assay or Taq-Man assay. RESULTS Two polymorphisms were associated with the risk of lung cancer in male smokers, as in female never smokers. Male smokers carrying the rs4975616 variant allele had a significantly decreased risk of lung cancer (in a codominant model: odds ratio, 0.77; 95% confidence interval, 0.61 to 0.96; p = 0.02). The rs9387478 polymorphism also reduced lung cancer risk in male smokers (in a codominant model: odds ratio, 0.85; 95% confidence interval, 0.73 to 0.997; p = 0.046). In a stratified analysis, the association between these polymorphisms and the risk of lung cancer was predominant in lighter smokers and for cases of adenocarcinoma. CONCLUSION These results suggest that a subset of polymorphisms known to be associated with the risk of lung cancer in female never smokers is also associated with the risk of lung cancer in male smokers.
Collapse
Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
- Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
| | - Won Kee Lee
- Biostatistics, Medical Research Collaboration Center, Kyungpook National University, Daegu, Korea
| | - Shin Yup Lee
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
- Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Jaehee Lee
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Seung Ick Cha
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Chang Ho Kim
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Eung Bae Lee
- Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jae Yong Park
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
- Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Korea
- Department of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
- Correspondence to Jae Yong Park, M.D. Lung Cancer Center, Kyungpook National University Chilgok Hospital, 807 Hoguk-ro, Buk-gu, Daegu 41404, Korea Tel: +82-53-200-2631 Fax: +82-53-200-2027 E-mail:
| |
Collapse
|
5
|
He Y, Shi J, Schmidt B, Liu Q, Shi G, Xu X, Liu C, Gao Z, Guo T, Shan B. Circulating Tumor Cells as a Biomarker to Assist Molecular Diagnosis for Early Stage Non-Small Cell Lung Cancer. Cancer Manag Res 2020; 12:841-854. [PMID: 32104066 PMCID: PMC7008188 DOI: 10.2147/cmar.s240773] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
Background and Objective Compared with tissue biopsy, liquid biopsy is the most preferable non-invasive promising method in personalized medicine, although it has many limitations in isolating circulating tumor cells (CTC). Lung cancer associated mortality is drastically increased due to a shortfall of early-stage detection, which remains a challenge. Herein, we aimed to detect lung cancer at an early-stage using CellCollector device. Methods 39,627 volunteers underwent low-dose computed tomography; 2508 cases with pulmonary nodules and 7080 with no pulmonary nodules were chosen. After follow-up, 24 patients were diagnosed with early-stage non-small cell lung cancer (NSCLC), and subjected to CTC detection using CellCollector, along with 72 healthy volunteers. Immunofluorescence staining for EpCAM/CKs and CD45 were performed for CTC validation. Results Fifteen out of twenty-four (stage I, n = 18; stage II, n = 6) early-stage lung cancer patients were found to be CTC-positive, whereas no CTC was found in the control group. Genetic mutation of TP53, ERBB2, PDGFRA, CFS1R and FGFR1 in the CTC revealed 71.6% of the mutation sites similar to the tumor tissues of 13 patients. Molecular characterization revealed higher expression of protein PD-LI in CTC (40%) as compared to tumor tissue (26.7%). Moreover, CTC clusters were detected in 40% of patients. Conclusion CTC detection using the CellCollector in early-stage NSCLC had a relative high capture rate. Moreover, CTC analysis is a prospective setting for molecular diagnostic in cases when tumor tissue biopsy is not desirable.
Collapse
Affiliation(s)
- Yutong He
- Cancer Institute, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Jin Shi
- Cancer Institute, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Bernd Schmidt
- Department of Internal Medicine - Pneumology and Sleep Medicine, Central Emergency Room, Palliative Medicine, DRK Kliniken Berlin, Berlin 13359, Germany
| | - Qingyi Liu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Gaofeng Shi
- Department of Radiology, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Xiaoli Xu
- Follow-Up Centre, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Congmin Liu
- Cancer Institute, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Zhaoyu Gao
- Cancer Institute, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Tiantian Guo
- Cancer Institute, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| | - Baoen Shan
- Cancer Institute, The Fourth Hospital of Hebei Medical University/The Tumor Hospital of Hebei Province, Shijiazhuang, Hebei 050011, People's Republic of China
| |
Collapse
|
6
|
Association between CSF1 and CSF1R Polymorphisms and Parkinson's Disease in Taiwan. J Clin Med 2019; 8:jcm8101529. [PMID: 31554150 PMCID: PMC6832167 DOI: 10.3390/jcm8101529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background: CSF1/CSF1R neuroinflammatory signaling is emerging as an important pathway involved in the pathogenesis of Parkinson’s disease (PD). However, the genetic associations between CSF1/CSF1R and PD have not yet been explored. Methods: We investigated the effects of two functional genetic variants, including CSF1 rs1058885 and CSF1R rs10079250 in a cohort including 502 Taiwanese patients with PD and 511 age- and gender-matched healthy controls. Results: The CSF1 rs1058885 TT genotype was less frequent in PD patients compared with control subjects (odds ratio (OR) = 0.63, 95% confidence interval (CI): 0.43–0.92, p = 0.015). The PD patients also had a lower frequency of the CSF1 rs1058885 T allele compared with the control subjects (OR = 0.80, 95% CI: 0.67–0.96, p = 0.014). No statistically significant differences in allelic and genotypic frequencies of CSF1R rs10079250 between the PD and control subjects were found, even after stratification by age at onset and gender. Conclusion: This study reports a genetic association between CSF1 and PD for the first time.
Collapse
|
7
|
Inamura K, Shigematsu Y, Ninomiya H, Nakashima Y, Kobayashi M, Saito H, Takahashi K, Futaya E, Okumura S, Ishikawa Y, Kanda H. CSF1R-Expressing Tumor-Associated Macrophages, Smoking and Survival in Lung Adenocarcinoma: Analyses Using Quantitative Phosphor-Integrated Dot Staining. Cancers (Basel) 2018; 10:cancers10080252. [PMID: 30065206 PMCID: PMC6115958 DOI: 10.3390/cancers10080252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
CSF1R-expressing tumor-associated macrophages (TAMs) induce a tumor-promoting microenvironment by regulating immunity. Evidence demonstrates that the expression and single nucleotide polymorphisms of CSF1R relate with survival and risk of lung cancer in never smokers. However, no previous studies have examined the association of CSF1R expression in TAMs with mortality or whether the prognostic association differs according to smoking status in lung adenocarcinoma. Quantitative phosphor-integrated dot staining was used to precisely assess CSF1R expression in TAMs. Using 195 consecutive cases of lung adenocarcinoma, we examined the association of CSF1R expression with mortality and whether the prognostic association differs according to smoking status. We observed high expression levels of CSF1R in TAMs in 65 of 195 (33%) cases of lung adenocarcinoma. High expression levels of CSF1R were associated with high lung cancer-specific mortality (log-rank p = 0.037; hazard ratio (HR) = 1.61, 95% confidence interval (CI) = 1.02−2.52, p = 0.043). This prognostic association differed according to smoking status (p for interaction = 0.049, between never-smoking and ever-smoking patients). The association between high expression levels of CSF1R and lung cancer-specific mortality was stronger in never-smoking patients (log-rank p = 0.0027; HR = 2.90, 95% CI = 1.41−6.11, p = 0.0041) than in ever-smoking patients (log-rank p = 0.73; HR = 1.11, 95% CI = 0.59−2.00, p = 0.73). The findings suggest that CSF1R-expressing TAMs may exert stronger tumor-promoting immunity in never-smoking patients with lung adenocarcinoma and serve as a therapeutic target in precision immunotherapies.
Collapse
Affiliation(s)
- Kentaro Inamura
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Yasuyuki Shigematsu
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Hironori Ninomiya
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Yasuhiro Nakashima
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Maki Kobayashi
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Haruyuki Saito
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc., 1 Sakura-machi, Hino, Tokyo 191-8511, Japan.
| | - Katsuhiro Takahashi
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc., 1 Sakura-machi, Hino, Tokyo 191-8511, Japan.
| | - Etsuko Futaya
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc., 1 Sakura-machi, Hino, Tokyo 191-8511, Japan.
| | - Sakae Okumura
- Department of Thoracic Surgical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Yuichi Ishikawa
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Hiroaki Kanda
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
- Department of Pathology, Saitama Cancer Center, 780 Komuro, Ina, Kitaadachi-gun, Saitama 362-0806, Japan.
| |
Collapse
|
8
|
Zhang W, Fan J, Chen Q, Lei C, Qiao B, Liu Q. SPP1 and AGER as potential prognostic biomarkers for lung adenocarcinoma. Oncol Lett 2018; 15:7028-7036. [PMID: 29849788 PMCID: PMC5962856 DOI: 10.3892/ol.2018.8235] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/05/2018] [Indexed: 11/23/2022] Open
Abstract
Overdue treatment and prognostic evaluation lead to low survival rates in patients with lung adenocarcinoma (LUAD). To date, effective biomarkers for prognosis are still required. The aim of the present study was to screen differentially expressed genes (DEGs) as biomarkers for prognostic evaluation of LUAD. DEGs in tumor and normal samples were identified and analyzed for Kyoto Encyclopedia of Genes and Genomes/Gene Ontology functional enrichments. The common genes that are up and downregulated were selected for prognostic analysis using RNAseq data in The Cancer Genome Atlas. Differential expression analysis was performed with 164 samples in GSE10072 and GSE7670 datasets. A total of 484 DEGs that were present in GSE10072 and GSE7670 datasets were screened, including secreted phosphoprotein 1 (SPP1) that was highly expressed and DEGs ficolin 3, advanced glycosylation end-product specific receptor (AGER), transmembrane protein 100 that were lowly expressed in tumor tissues. These four key genes were subsequently verified using an independent dataset, GSE19804. The gene expression model was consistent with GSE10072 and GSE7670 datasets. The dysregulation of highly expressed SPP1 and lowly expressed AGER significantly reduced the median survival time of patients with LUAD. These findings suggest that SPP1 and AGER are risk factors for LUAD, and these two genes may be utilized in the prognostic evaluation of patients with LUAD. Additionally, the key genes and functional enrichments may provide a reference for investigating the molecular expression mechanisms underlying LUAD.
Collapse
Affiliation(s)
- Weiguo Zhang
- Henan Key Laboratory of Cancer Epigenetics, Department of Oncology Surgery, Cancer Institute and College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Junli Fan
- Henan Key Laboratory of Cancer Epigenetics, Department of Oncology Surgery, Cancer Institute and College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Qiang Chen
- Henan Key Laboratory of Cancer Epigenetics, Department of Oncology Surgery, Cancer Institute and College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Caipeng Lei
- Henan Key Laboratory of Cancer Epigenetics, Department of Oncology Surgery, Cancer Institute and College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Bin Qiao
- Henan Key Laboratory of Cancer Epigenetics, Department of Oncology Surgery, Cancer Institute and College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Qin Liu
- Henan Key Laboratory of Cancer Epigenetics, Department of Oncology Surgery, Cancer Institute and College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| |
Collapse
|
9
|
Zhang MY, Liu XX, Li H, Li R, Liu X, Qu YQ. Elevated mRNA Levels of AURKA, CDC20 and TPX2 are associated with poor prognosis of smoking related lung adenocarcinoma using bioinformatics analysis. Int J Med Sci 2018; 15:1676-1685. [PMID: 30588191 PMCID: PMC6299412 DOI: 10.7150/ijms.28728] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/11/2018] [Indexed: 01/10/2023] Open
Abstract
Background and aim: Adenocarcinoma is a very common pathological subtype for lung cancer. We aimed to identify the gene signature associated with the prognosis of smoking related lung adenocarcinoma using bioinformatics analysis. Methods: A total of five gene expression profiles (GSE31210, GSE32863, GSE40791, GSE43458 and GSE75037) have been identified from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were analyzed using GEO2R software and functional and pathway enrichment analysis. Furthermore, the overall survival (OS) and recurrence-free survival (RFS) have been validated using an independent cohort from the Cancer Genome Atlas (TCGA) database. Results: We identified a total of 58 DEGs which mainly enriched in ECM-receptor interaction, platelet activation and PPAR signaling pathway. Then according to the enrichment analysis results, we selected three genes (AURKA, CDC20 and TPX2) for their roles in regulating tumor cell cycle and cell division. The results showed that the hazard ratio (HR) of the mRNA expression of AURKA for OS was 1.588 with (1.127-2.237) 95% confidence interval (CI) (P=0.009). The mRNA levels of CDC20 (HR 1.530, 95% CI 1.086-2.115, P=0.016) and TPX2 (HR 1.777, 95%CI 1.262-2.503, P=0.001) were also significantly associated with the OS. Expression of these three genes were not associated with RFS, suggesting that there might be many factors affect RFS. Conclusion: The mRNA signature of AURKA, CDC20 and TPX2 were potential biomarkers for predicting poor prognosis of smoking related lung adenocarcinoma.
Collapse
Affiliation(s)
- Meng-Yu Zhang
- Department of Respiratory Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiao-Xia Liu
- Department of Respiratory Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Hao Li
- Department of Respiratory Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Rui Li
- Department of Respiratory Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiao Liu
- Department of Respiratory Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yi-Qing Qu
- Department of Respiratory Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| |
Collapse
|
10
|
Li G, Mei Y, Yang F, Yi S, Wang L. Identification of genome variations in patients with lung adenocarcinoma using whole genome re‑sequencing. Mol Med Rep 2017; 16:9464-9472. [PMID: 29039585 PMCID: PMC5780004 DOI: 10.3892/mmr.2017.7805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 04/27/2017] [Indexed: 12/30/2022] Open
Abstract
Lung adenocarcinoma is one of the types of non-small cell lung carcinoma, which tends to be treated with surgical therapy rather than radiation therapy. It occurs in smokers and non-smokers, and is the most common form of lung cancer among non-smokers and women. Gene rearrangements, including ALK, ROS1 and RET, and gene mutations, including epidermal growth factor receptor (EGFR), HER2, Kristen rat sarcoma viral oncogene homolog, BRAF, phosphoinositide-3-kinase, catalytic, α polypeptide and MET, have been identified in lung adenocarcinoma, which enable targeted therapy in lung adenocarcinoma, for example erlotinib, gefitinib and afatinib, which are EGFR inhibitors. The aim of the present study was to further investigate genome variations in lung adenocarcinoma. Single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs) and copy number variations (CNVs) were identified in the whole genome from four patients with adenocarcinoma using a whole genome re-sequencing method performed on the Illumina HiSeq Xten platform. In total, ~415 GB of clean reads were obtained, the average sequencing depth was 31.10-fold, and 99.29% of the reference genome was covered by the clean reads. An average of 3,364,270 SNPs was identified, 98.76% of which were matched to the SNP database (dbSNP), and an average of 453,547 InDels were identified, 28.28% of which were in the dbSNP. The present study also identified a total of 13,050 SVs and 886 CNVs. The majority of the SVs were deletions (74.25%) and the major CNVs were in intergenic regions and coding sequence regions. In conclusion, the results of the present study generated an output of the genome alterations in lung adenocarcinoma, and provided a foundation for further investigation of the pathogenesis of lung adenocarcinoma.
Collapse
Affiliation(s)
- Guiyuan Li
- Department of Oncology, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Yunqing Mei
- Department of Thoracic Cardiovascular Surgery, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Fan Yang
- Department of Clinical Laboratory Medicine, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Shengming Yi
- Department of Oncology, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Lemin Wang
- Department of Cardiology, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China
| |
Collapse
|
11
|
Yeh YM, Hsu SJ, Lin PC, Hsu KF, Wu PY, Su WC, Chang JY, Shen MR. The c.1085A>G Genetic Variant of CSF1R Gene Regulates Tumor Immunity by Altering the Proliferation, Polarization, and Function of Macrophages. Clin Cancer Res 2017; 23:6021-6030. [PMID: 28724665 DOI: 10.1158/1078-0432.ccr-17-1007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/27/2017] [Accepted: 07/14/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Targeting tumor-associated macrophages with colony-stimulating factor 1 receptor (CSF-1R) inhibition reveals a strategy for cancer therapy. Here, we studied the impact of CSF1R germline genetic variant on CSF-1R signaling and the susceptibility to CSF-1R inhibitors.Experimental designs:CSF1R germline genetic variants were studied in 140 cancer patients. CSF-1R phosphorylation, endocytosis, and macrophage polarization were measured as the response to CSF-1 stimulation. Tumor-associated macrophages in surgical specimens and sensitivity to CSF-1R inhibitors were used to determine macrophage function.Results: A CSF1R c.1085A>G genetic variant causing the change of histidine to arginine in the domain of receptor dimerization was identified as a high allele frequency in Eastern Asian population. Cancer patients with this variant allele had less M2-like tumor-associated macrophages accompanied by low VEGF expression in tumor tissues. Importantly, CSF1R genetic variant was significantly associated with disease-free survival in colorectal, endometrial, and ovarian cancer. In terms of differentiation, macrophages with CSF1R c.1085A>G genetic variant displayed a refractory response to CSF-1 stimulation and macrophage survival was sensitive to CSF-1R inhibitors with IC50 of 0.1 to 1 nmol/L range. On contrast, CSF-1 induced a prominent phosphorylation and rapid endocytosis of CSF-1R, leading to an M2-like dominant polarization in macrophages with CSF1R c.1085 genotype A_A, in which CSF-1R inhibitors of PLX3397, BLZ945, and GW2580 inhibited macrophage survival with IC50 of 10 to 100 nmol/L range.Conclusions: The CSF1R c.1085A>G genetic variant regulates tumor immunity by altering the polarization and function of macrophages. This genetic variant confers the sensitivity to CSF-1R inhibitors, implying as a biomarker in targeting CSF-1R signaling for cancer treatment. Clin Cancer Res; 23(20); 6021-30. ©2017 AACR.
Collapse
Affiliation(s)
- Yu-Min Yeh
- Graduate Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.,Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Shan-Ju Hsu
- Department of Pharmacology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Peng-Chan Lin
- Graduate Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.,Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Keng-Fu Hsu
- Graduate Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.,Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Pei-Ying Wu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Jang-Yang Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Meng-Ru Shen
- Department of Pharmacology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan. .,Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| |
Collapse
|
12
|
Yoo SS, Kang HG, Choi JE, Do SK, Lee WK, Choi SH, Lee SY, Lee SY, Lee J, Cha SI, Kim CH, Seok Y, Lee E, Kim MS, Lee JM, Cho HJ, Oh IJ, Kim YC, Cho S, Jheon S, Jung CY, Kim MH, Lee MK, Park JY. Effects of polymorphisms identified in genome-wide association studies of never-smoking females on the prognosis of non-small cell lung cancer. Cancer Genet 2017; 212-213:8-12. [PMID: 28449811 DOI: 10.1016/j.cancergen.2017.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/20/2017] [Accepted: 03/09/2017] [Indexed: 01/13/2023]
Abstract
A number of genome-wide association studies have reported several variants that influence the risk of lung cancer in never-smoking females. We evaluated the impact of these variants on survival outcome in never-smoking females with non-small cell lung cancer (NSCLC). In total, 510 never-smoking females with NSCLC who underwent curative surgery were enrolled. Eleven variants associated with lung cancer susceptibility in never-smoking females were genotyped and their associations with survival outcome were analyzed. Among these 11 variants, TP63 rs7631358 and CSF1R rs10079250 affected survival outcomes. TP63 rs7631358 G > A was associated with a relatively worse overall survival (under a dominant model; hazard ratio = 2.31, 95% confidence interval = 1.18-4.52, P = 0.01). CSF1R rs10079250 A > G was associated with a relatively better disease-free survival (under a codominant model; hazard ratio = 0.70, 95% confidence interval = 0.53-0.93, P = 0.01). These results suggest that TP63 rs7631358 G > A and CSF1R rs10079250 A > G may affect the prognosis of NSCLC in never-smoking females, as well as the risk of lung cancer.
Collapse
Affiliation(s)
- Seung Soo Yoo
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Hyo-Gyoung Kang
- Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, South Korea; Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Jin Eun Choi
- Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, South Korea; Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Sook Kyung Do
- Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Won Kee Lee
- Preventive Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Sun Ha Choi
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - So Yeon Lee
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Shin Yup Lee
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Jaehee Lee
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Seung Ick Cha
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Chang Ho Kim
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Yangki Seok
- Thoracic Surgery, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Eungbae Lee
- Thoracic Surgery, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Moon Soo Kim
- Center for Lung Cancer, National Cancer Center, Goyang, South Korea
| | - Jong Mog Lee
- Center for Lung Cancer, National Cancer Center, Goyang, South Korea
| | - Hyun-Ju Cho
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Chonnam, South Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Chonnam, South Korea
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Chonnam, South Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, South Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, South Korea
| | - Chi Young Jung
- Department of Internal Medicine, Catholic University of Daegu, School of Medicine, Daegu, South Korea
| | - Mi-Hyun Kim
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, South Korea
| | - Min Ki Lee
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, South Korea
| | - Jae Yong Park
- Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea; Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, South Korea.
| |
Collapse
|
13
|
Lee SY, Kang HG, Choi JE, Jung DK, Lee WK, Lee HC, Lee SY, Yoo SS, Lee J, Seok Y, Lee EB, Cha SI, Cho S, Kim CH, Lee MH, Park JY. Polymorphisms in cancer-related pathway genes and lung cancer. Eur Respir J 2016; 48:1184-1191. [DOI: 10.1183/13993003.02040-2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 07/01/2016] [Indexed: 12/13/2022]
Abstract
We evaluated the associations between potentially functional variants in a comprehensive list of cancer-related genes and lung cancer in a Korean population.A total of 1969 potentially functional single nucleotide polymorphisms (SNPs) of 1151 genes involved in carcinogenesis were evaluated using an Affymetrix custom-made GeneChip in 610 nonsmall cell lung cancer patients and 610 healthy controls. A replication study was conducted in an independent set of 490 cases and 486 controls. 68 SNPs were significantly associated with lung cancer in the discovery set and tested for replication.Among the 68 SNPs, three SNPs (corepressor interacting with RBPJ 1 (CIR1) rs13009079T>C, ribonucleotide reductase M1 (RRM1) rs1465952T>C and solute carrier family 38, member 4 (SLC38A4) rs2429467C>T) consistantly showed significant associations with lung cancer in the replication study. In combined analysis, adjusted odds ratio for CIR1 rs13009079T>C, RRM1 rs1465952T>C and SLC38A4 rs2429467C>T were 0.69, 0.71 and 0.73, respectively (p=4×10−5, 0.01 and 0.001, respectively) under the dominant model. The relative mRNA expression level of CIR1 was significantly associated with rs13009079T>C genotypes in normal lung tissues (ptrend=0.03).These results suggest that the three SNPs, particularly CIR1 rs13009079T>C, may play a role in the pathogenesis of lung cancer.
Collapse
|
14
|
Pradel LP, Ooi CH, Romagnoli S, Cannarile MA, Sade H, Rüttinger D, Ries CH. Macrophage Susceptibility to Emactuzumab (RG7155) Treatment. Mol Cancer Ther 2016; 15:3077-3086. [DOI: 10.1158/1535-7163.mct-16-0157] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/12/2016] [Accepted: 08/18/2016] [Indexed: 11/16/2022]
|
15
|
Choi JR, Park SY, Noh OK, Koh YW, Kang DR. Gene mutation discovery research of non-smoking lung cancer patients due to indoor radon exposure. Ann Occup Environ Med 2016; 28:13. [PMID: 26985396 PMCID: PMC4793700 DOI: 10.1186/s40557-016-0095-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/18/2016] [Indexed: 11/10/2022] Open
Abstract
Although the incidence and mortality for most cancers such as lung and colon are decreasing in several countries, they are increasing in several developed countries because of an unhealthy western lifestyles including smoking, physical inactivity and consumption of calorie-dense food. The incidences for lung and colon cancers in a few of these countries have already exceeded those in the United States and other western countries. Among them, lung cancer is the main cause of cancer death in worldwide. The cumulative survival rate at five years differs between 13 and 21 % in several countries. Although the most important risk factors are smoking for lung cancer, however, the increased incidence of lung cancer in never smokers(LCINS) is necessary to improve knowledge concerning other risk factors. Environmental factors and genetic susceptibility are also thought to contribute to lung cancer risk. Patients with lung adenocarcinoma who have never smoking frequently contain mutation within tyrosine kinase domain of the epidermal growth factor receptor(EGFR) gene. Also, K-ras mutations are more common in individuals with a history of smoking use and are related with resistance to EFGR-tyrosine kinase inhibitors. Recently, radon(Rn), natural and noble gas, has been recognized as second common reason of lung cancer. In this review, we aim to know whether residential radon is associated with an increased risk for developing lung cancer and regulated by several genetic polymorphisms.
Collapse
Affiliation(s)
- Jung Ran Choi
- Department of Bio-resource engineering, College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Seong Yong Park
- Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - O Kyu Noh
- Department of Radiation Oncology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Young Wha Koh
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Dae Ryong Kang
- Department of Humanities and Social Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| |
Collapse
|
16
|
Niu T, Liu N, Yu X, Zhao M, Choi HJ, Leo PJ, Brown MA, Zhang L, Pei YF, Shen H, He H, Fu X, Lu S, Chen XD, Tan LJ, Yang TL, Guo Y, Cho NH, Shen J, Guo YF, Nicholson GC, Prince RL, Eisman JA, Jones G, Sambrook PN, Tian Q, Zhu XZ, Papasian CJ, Duncan EL, Uitterlinden AG, Shin CS, Xiang S, Deng HW. Identification of IDUA and WNT16 Phosphorylation-Related Non-Synonymous Polymorphisms for Bone Mineral Density in Meta-Analyses of Genome-Wide Association Studies. J Bone Miner Res 2016; 31:358-68. [PMID: 26256109 PMCID: PMC5362379 DOI: 10.1002/jbmr.2687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 11/06/2022]
Abstract
Protein phosphorylation regulates a wide variety of cellular processes. Thus, we hypothesize that single-nucleotide polymorphisms (SNPs) that may modulate protein phosphorylation could affect osteoporosis risk. Based on a previous conventional genome-wide association (GWA) study, we conducted a three-stage meta-analysis targeting phosphorylation-related SNPs (phosSNPs) for femoral neck (FN)-bone mineral density (BMD), total hip (HIP)-BMD, and lumbar spine (LS)-BMD phenotypes. In stage 1, 9593 phosSNPs were meta-analyzed in 11,140 individuals of various ancestries. Genome-wide significance (GWS) and suggestive significance were defined by α = 5.21 × 10(-6) (0.05/9593) and 1.00 × 10(-4), respectively. In stage 2, nine stage 1-discovered phosSNPs (based on α = 1.00 × 10(-4)) were in silico meta-analyzed in Dutch, Korean, and Australian cohorts. In stage 3, four phosSNPs that replicated in stage 2 (based on α = 5.56 × 10(-3), 0.05/9) were de novo genotyped in two independent cohorts. IDUA rs3755955 and rs6831280, and WNT16 rs2707466 were associated with BMD phenotypes in each respective stage, and in three stages combined, achieving GWS for both FN-BMD (p = 8.36 × 10(-10), p = 5.26 × 10(-10), and p = 3.01 × 10(-10), respectively) and HIP-BMD (p = 3.26 × 10(-6), p = 1.97 × 10(-6), and p = 1.63 × 10(-12), respectively). Although in vitro studies demonstrated no differences in expressions of wild-type and mutant forms of IDUA and WNT16B proteins, in silico analyses predicts that WNT16 rs2707466 directly abolishes a phosphorylation site, which could cause a deleterious effect on WNT16 protein, and that IDUA phosSNPs rs3755955 and rs6831280 could exert indirect effects on nearby phosphorylation sites. Further studies will be required to determine the detailed and specific molecular effects of these BMD-associated non-synonymous variants.
Collapse
Affiliation(s)
- Tianhua Niu
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Ning Liu
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Xun Yu
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Ming Zhao
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Hyung Jin Choi
- Dept of Internal Medicine, College of Medicine, Seoul National University, Seoul, Korea
- Dept of Internal Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Paul J. Leo
- University of Queensland Diamantina Inst, Translat Res Inst, Brisbane, Queensland, Australia
| | - Matthew A. Brown
- University of Queensland Diamantina Inst, Translat Res Inst, Brisbane, Queensland, Australia
| | - Lei Zhang
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
- Ctr of Syst Biomed Sci, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Yu-Fang Pei
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Hui Shen
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Hao He
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Xiaoying Fu
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Shan Lu
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Xiang-Ding Chen
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Li-Jun Tan
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Tie-Lin Yang
- School of Life Sci & Tech, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Yan Guo
- School of Life Sci & Tech, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Nam H. Cho
- Dept of Prev Med, Ajou University School of Medicine, Youngtong-Gu, Suwon, Korea
| | - Jie Shen
- Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Yan-Fang Guo
- Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, P. R. China
| | | | - Richard L. Prince
- School of Medicine and Pharmacology, University of Western Australia, Perth, Australia
- Dept of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Perth, Australia
| | - John A. Eisman
- Garvan Inst of Medical Research, University of New South Wales, Sydney, Australia
| | - Graeme Jones
- Menzies Res Inst, University of Tasmania, Hobart, Australia
| | - Philip N. Sambrook
- Kolling Inst, Royal North Shore Hospital, University of Sydney, Sydney, Australia
| | - Qing Tian
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Xue-Zhen Zhu
- School of Life Sci & Tech, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | | | - Emma L. Duncan
- University of Queensland Diamantina Inst, Translat Res Inst, Brisbane, Queensland, Australia
- Endocrinology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - André G. Uitterlinden
- Dept of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Dept of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Chan Soo Shin
- Dept of Internal Medicine, College of Medicine, Seoul National University, Seoul, Korea
| | - Shuanglin Xiang
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Hong-Wen Deng
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| |
Collapse
|
17
|
Choi YY, Lee SY, Lee WK, Jeon HS, Lee EB, Lee HC, Choi JE, Kang HG, Lee EJ, Bae EY, Yoo SS, Lee J, Cha SI, Kim CH, Kim IS, Lee MH, Kim YT, Jheon S, Park JY. RACK1 is a candidate gene associated with the prognosis of patients with early stage non-small cell lung cancer. Oncotarget 2015; 6:4451-66. [PMID: 25686824 PMCID: PMC4414203 DOI: 10.18632/oncotarget.2865] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/07/2014] [Indexed: 01/10/2023] Open
Abstract
Background This study was conducted to identify genetic polymorphisms associated with the prognosis of patients with early stage NSCLC. Materials and Methods We genotyped 1,969 potentially functional single nucleotide polymorphisms (SNPs) of 1,151 genes involved in carcinogenesis in 166 NSCLC patients who underwent curative surgery, using the Affymetrix custom-made GeneChip. A replication study was performed in an independent cohort of 626 patients. Results Fifty six SNPs which were associated with both overall survival (OS) and disease-free survival (DFS) with log-rank P values < 0.05 in discovery set were selected for validation. Among those, five SNPs (RACK1 rs1279736C>A and rs3756585T>G, C3 rs2287845T>C, PCAF rs17006625A>G, and PCM1 rs17691523C>G) were found to be significantly associated with survival in the same direction as the discovery set. In combined analysis, the rs1279736C>A and rs3756585T>G were most significantly associated with OS and DFS in multivariate analysis (P for OS = 4 × 10−5 and 7 × 10−5, respectively; and P for DFS = 0.003, both; under codominant model). In vitro promoter assay and electrophoretic mobility shift assay revealed that the rs3756585 T-to-G change increased promoter activity and transcription factor binding of RACK1. Conclusions We identified five SNPs, especially RACK1 rs3756585T>G, as markers for prognosis of patients with surgically resected NSCLC.
Collapse
Affiliation(s)
- Yi-Young Choi
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Shin Yup Lee
- Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Won Kee Lee
- Biostatistics Center, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyo-Sung Jeon
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea.,Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Eung Bae Lee
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea.,Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyun Cheol Lee
- Diagnosis and Prediction Biotechnology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jin Eun Choi
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea.,Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Hyo-Gyoung Kang
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Jin Lee
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Eun Young Bae
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Soo Yoo
- Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jaehee Lee
- Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Ick Cha
- Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Kim
- Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - In-San Kim
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Myung Hoon Lee
- Diagnosis and Prediction Biotechnology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Jae Yong Park
- Departments of Biochemistry and Cell Biology, Kyungpook National University, Daegu, Republic of Korea.,Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| |
Collapse
|